Queen remained on as pitching coach under Johnson and the two reportedly feuded extensively, despite Johnson's reputation as a good communicator. Johnson also had rumoured differences with several of his players, including Pat Hentgen, Ed Sprague, and Cy Young Award winner Roger Clemens, all of whom left the team after the 1998 season.

Despite this lack of chemistry, Johnson guided the 1998 Blue Jays to a respectable third-place finish in the AL East with an 88–74 record, just four games out of a tie for the wild card. It was the team's first winning season since they won two World Series in a row in 1992 and 1993.

This success was partly attributed to the stories Johnson would tell his players about his battle experiences in the Vietnam War. For example, he told Hentgen a story about his war experiences to get him to accept a different place in the pitching rotation.[1]

However, in late November, Johnson told several Toronto newspapers that all of these stories were completely made up. In truth, Johnson had been in the Marine Corps reserves throughout the war, and trained mortarmen at Camp Pendleton while playing in the Dodgers' farm system. He'd also claimed for over 20 years that he'd been an All-American high school basketball player, and turned down a scholarship to attend UCLA.[2]

During the 1998 baseball winter meetings, Johnson said that admitting the truth was like having "a 50,000 pound weight" taken off his shoulders. He said he'd lied because he felt guilty about going to spring training with the Dodgers while many of his friends fought in the war. He entered therapy, and called several of his players to apologize for lying. [3]

The Blue Jays were initially willing to stand by Johnson and let him return for 1999. During spring training, he apologized to the entire team, and later said that he didn't seem to detect a credibility problem. However, the next month brought a steady diet of questions about Johnson's credibility, as well as outside attacks (Sprague, for instance, called Johnson a "liar" and a "backstabber"). Finally, on March 17, less than a month before opening day, Blue Jays general manager Gord Ash fired Johnson and replaced him with Jim Fregosi. Ash said that Johnson's presence had become so much of a distraction that he felt he would have to fire Johnson "if not now ... 30 or 45 days from now." He decided that he had to act in order to save the season.[4] In the years since Johnson's one season at the helm, the Blue Jays have failed to equal or better record than Johnson's 88–74 mark until 2015.[5]

In 2003, Johnson became manager of the Lincoln Saltdogs of the Northern League. In 2006, the Lincoln team joined the American Association of Independent Professional Baseball. On September 25, 2008, Johnson resigned after six years. His career record as the Saltdogs' manager was 315–255.